IFC, Ed Board
Publication date: March 2018Source: Epidemics, Volume 22Author(s): (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
The RAPIDD Ebola forecasting challenge special issue: Preface
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Cécile Viboud, Lone Simonsen, Gerardo Chowell, Alessandro Vespignani (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
The RAPIDD Ebola forecasting challenge: Model description and synthetic data generation
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Marco Ajelli, Qian Zhang, Kaiyuan Sun, Stefano Merler, Laura Fumanelli, Gerardo Chowell, Lone Simonsen, Cecile Viboud, Alessandro VespignaniAbstractThe Ebola forecasting challenge organized by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Fogarty International Center relies on synthetic disease datasets generated by numerical simulations of a highly detailed spatially-structured agent-based model. We discuss here the architecture and technical steps of the challenge, leading to datasets that mimic as much as possible the da...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Cécile Viboud, Kaiyuan Sun, Robert Gaffey, Marco Ajelli, Laura Fumanelli, Stefano Merler, Qian Zhang, Gerardo Chowell, Lone Simonsen, Alessandro Vespignani, the RAPIDD Ebola Forecasting Challenge groupAbstractInfectious disease forecasting is gaining traction in the public health community; however, limited systematic comparisons of model performance exist. Here we present the results of a synthetic forecasting challenge inspired by the West African Ebola crisis in 2014–2015 and involving 16 international academic teams and US government agencies, and co...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Application of the CDC EbolaResponse Modeling tool to disease predictions
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Robert H. Gaffey, Cécile ViboudAbstractModel-based predictions were critical in eliciting a vigorous international public health response to the 2014 Ebola Virus Disease outbreak in West Africa. Here, we describe the performances of an extension of the CDC-initiated EbolaResponse Modeling tool to the Ebola Forecasting Challenge, which offered a controlled environment for epidemiological predictions. In the EbolaResponse tool, transmission risks and proportions of population affected by interventions were fitted to data via least square fitting. Prediction ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Robust qualitative estimation of time-varying contact rates in uncertain epidemics
Publication date: Available online 15 March 2018Source: EpidemicsAuthor(s): Marco Tulio Angulo, Jorge X. Velasco-HernandezAbstractWe will inevitably face new epidemics where the lack of long time-series data and the uncertainty about the outbreak dynamics make difficult to obtain quantitative predictions. Here we present an algorithm to qualitatively infer time-varying contact rates from short time-series data, letting us predict the start, relative magnitude and decline of epidemic outbreaks. Using real time-series data of measles, dengue, and the current zika outbreak, we demonstrate our algorithm can outperform existing...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Transmission dynamics of influenza in two major cities of Uganda
Publication date: Available online 19 March 2018Source: EpidemicsAuthor(s): Wan Yang, Matthew J. Cummings, Barnabas Bakamutumaho, John Kayiwa, Nicholas Owor, Barbara Namagambo, Timothy Byaruhanga, Julius J. Lutwama, Max R. O’Donnell, Jeffrey ShamanAbstractIn this paper, we report the epidemic characteristics of the three co-circulating influenza viruses (i.e., A/H1N1, A/H3N2, and B) in two tropical African cities—Kampala and Entebbe, Uganda—over an eight-year period (2008–2015). Using wavelet methods, we show that influenza epidemics recurred annually during the study period. In most months, two or more influenza v...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Contagion! The BBC Four Pandemic – The model behind the documentary
Publication date: Available online 22 March 2018Source: EpidemicsAuthor(s): Petra Klepac, Stephen Kissler, Julia GogAbstractTo mark the centenary of the 1918 influenza pandemic, the broadcasting network BBC have put together a 75-min documentary called ‘Contagion! The BBC Four Pandemic’. Central to the documentary is a nationwide citizen science experiment, during which volunteers in the United Kingdom could download and use a custom mobile phone app called BBC Pandemic, and contribute their movement and contact data for a day.As the ‘maths team’, we were asked to use the data from the app to build and run a model ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Age difference between heterosexual partners in Britain: Implications for the spread of Chlamydia trachomatis
This study illustrates how sexual behavior data can be used to reconstruct detailed sexual mixing patterns by age, and how these patterns can be integrated into dynamic transmission models. The proposed framework can be extended to study the effects of age-dependent transmission on incidence in any STI. (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Using state-space models to predict the abundance of juvenile and adult sea lice on Atlantic salmon
In this study, two sets of multivariate autoregressive state-space models were applied to Chilean sea lice data from six Atlantic salmon production cycles on five isolated farms (at least 20 km seaway distance away from other known active farms), to evaluate the utility of these models for predicting sea lice abundance over time on farms. The models were constructed with different parameter configurations, and the analysis demonstrated large heterogeneity between production cycles for the autoregressive parameter, the effects of chemotherapeutant bath treatments, and the process-error variance. A model allowing for diffe...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Role of animal movement and indirect contact among farms in transmission of porcine epidemic diarrhea virus
Publication date: Available online 12 April 2018Source: EpidemicsAuthor(s): Kimberly VanderWaal, Andres Perez, Montse Torremorrell, Robert M. Morrison, Meggan CraftAbstractEpidemiological models of the spread of pathogens in livestock populations primarily focus on direct contact between farms based on animal movement data, and in some cases, local spatial spread based on proximity between premises. The roles of other types of indirect contact among farms is rarely accounted for. In addition, data on animal movements is seldom available in the United States. However, the spread of porcine epidemic diarrhea virus (PEDv) in ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Epidemics on dynamic networks
We describe recent advances in they apply to infection processes, considering all of the methods used to record, measure and analyse them, and their implications for disease transmission. Finally, we outline some key challenges and opportunities in the field. (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
A model for leptospire dynamics and control in the Norway rat (Rattus norvegicus) the reservoir host in urban slum environments
Publication date: Available online 5 May 2018Source: EpidemicsAuthor(s): Amanda Minter, Peter J. Diggle, Federico Costa, James Childs, Albert I. Ko, Mike BegonAbstractLeptospirosis is a zoonosis that humans can contract via contact with animal reservoirs directly or with water contaminated with their urine. The primary reservoir of pathogenic leptospires within urban slum environments is the Norway rat (Rattus norvegicus). Motivated by the annual outbreaks of human leptospirosis in slum urban settings, the within population infection dynamics of the Norway rat were investigated in Pau da Lima, an community in Salvador, Bra...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Concurrency of partnerships, consistency with data, and control of sexually transmitted infections
Publication date: Available online 14 May 2018Source: EpidemicsAuthor(s): Trystan Leng, Matt J. KeelingAbstractSexually transmitted infections (STIs) are a globally increasing public health problem. Mathematical models, carefully matched to available epidemiological and behavioural data, have an important role to play in predicting the action of control measures. Here, we explore the effect of concurrent sexual partnerships on the control of a generic STI with susceptible-infected-susceptible dynamics. Concurrency refers to being in more than one sexual partnership at the same time, and is difficult to measure accurately. ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns
Publication date: Available online 17 May 2018Source: EpidemicsAuthor(s): Noémie Courtejoie, Henrik Salje, Benoît Durand, Gina Zanella, Simon CauchemezAbstractBluetongue virus is a vector-borne pathogen affecting ruminants that has caused major epidemics in France. Reconstructing the history of bluetongue in French cattle under control strategies such as vaccination has been hampered by the high level of sub-clinical infection, incomplete case data and poor understanding of vaccine uptake over time and space. To tackle these challenges, we used three age-structured serological surveys carried out in cattle (N = 22,34...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
